# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:10:24 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2~{S})-2-azanyl-3-cyclopentyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCCC1)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 XYC  XYC  '(2~{S})-2-azanyl-3-cyclopentyl-propanoic acid'  L-peptide  25  11  .  2017-07-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_XYC
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 XYC  O    O  O      0  -0.603  0.6221  20.8924  103.3591
 XYC  C    C  C      0   0.383  1.0795  21.8281  104.0449
 XYC  CA   C  CH1    0  -0.213  2.4861  22.3692  103.6719
 XYC  N    N  NH2    0  -0.785  3.2729  21.5148  102.7932
 XYC  CB   C  CH2    0  -0.419  2.3356  23.7617  103.0526
 XYC  C04  C  CH1    0  -0.242  3.6416  24.4849  102.7152
 XYC  C08  C  CH2    0  -0.433  3.3684  25.8813  102.1440
 XYC  C07  C  CH2    0  -0.450  3.1170  26.7730  103.3729
 XYC  C06  C  CH2    0  -0.450  3.8153  26.0612  104.5545
 XYC  C05  C  CH2    0  -0.439  4.4860  24.8209  103.9473
 XYC  HA   H  HCH1   0   0.204  3.0453  22.4733  104.6094
 XYC  H    H  HNH2   0   0.330  3.4007  20.6170  103.2451
 XYC  H2   H  HNH2   0   0.319  2.7085  21.3031  101.9776
 XYC  H6   H  HCH2   0   0.219  1.7342  24.3758  103.7279
 XYC  H7   H  HCH2   0   0.206  1.7478  23.6702  102.1299
 XYC  H8   H  HCH1   0   0.216  4.2070  23.8729  102.0093
 XYC  H9   H  HCH2   0   0.220  4.2520  26.2315  101.6038
 XYC  H10  H  HCH2   0   0.220  2.5362  25.8954  101.4366
 XYC  H11  H  HCH2   0   0.224  3.5021  27.7818  103.2184
 XYC  H12  H  HCH2   0   0.222  2.0479  26.8786  103.5644
 XYC  H13  H  HCH2   0   0.225  4.5384  26.7062  105.0556
 XYC  H14  H  HCH2   0   0.221  3.0850  25.7715  105.3124
 XYC  H15  H  HCH2   0   0.225  4.5764  23.9977  104.6589
 XYC  H16  H  HCH2   0   0.219  5.5015  25.0674  103.6243
 XYC  OXT  O  OC    -1  -0.619  0.5127  22.3998  105.0012

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 XYC  C08  C04  single  1.533  0.020  1.533
 XYC  C08  C07  single  1.539  0.020  1.539
 XYC  N    CA   single  1.458  0.019  1.458
 XYC  C04  CB   single  1.530  0.020  1.530
 XYC  C04  C05  single  1.531  0.020  1.531
 XYC  CB   CA   single  1.521  0.033  1.521
 XYC  C07  C06  single  1.546  0.020  1.546
 XYC  O    C    deloc   1.231  0.020  1.231
 XYC  CA   C    single  1.525  0.021  1.525
 XYC  C05  C06  single  1.535  0.020  1.535
 XYC  CA   HA   single  0.970  0.020  0.970
 XYC  N    H    single  0.860  0.020  0.860
 XYC  N    H2   single  0.890  0.020  1.040
 XYC  CB   H6   single  0.970  0.020  1.090
 XYC  CB   H7   single  0.970  0.020  1.090
 XYC  C04  H8   single  0.970  0.020  1.090
 XYC  C08  H9   single  0.970  0.020  1.090
 XYC  C08  H10  single  0.970  0.020  1.090
 XYC  C07  H11  single  0.970  0.020  1.090
 XYC  C07  H12  single  0.970  0.020  1.090
 XYC  C06  H13  single  0.970  0.020  1.090
 XYC  C06  H14  single  0.970  0.020  1.090
 XYC  C05  H15  single  0.970  0.020  1.090
 XYC  C05  H16  single  0.970  0.020  1.090
 XYC  C    OXT  deloc   1.250  0.020  1.250

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 XYC  OXT  C    CA   115.80  3.000
 XYC  OXT  C    O    126.70  3.000
 XYC  CA   C    O    120.80  1.700
 XYC  HA   CA   CB   109.00  3.000
 XYC  HA   CA   N    110.00  3.000
 XYC  CB   CA   N    110.40  1.500
 XYC  HA   CA   C    109.00  3.000
 XYC  CB   CA   C    110.50  1.500
 XYC  N    CA   C    111.00  2.800
 XYC  H2   N    H    104.11  3.000
 XYC  H2   N    CA   107.88  3.000
 XYC  H    N    CA   114.00  3.000
 XYC  H7   CB   H6   105.74  3.000
 XYC  H7   CB   C04  108.12  3.000
 XYC  H6   CB   C04  109.89  3.000
 XYC  H7   CB   CA   108.47  3.000
 XYC  H6   CB   CA   108.36  3.000
 XYC  C04  CB   CA   115.79  3.000
 XYC  H8   C04  C05  110.95  3.000
 XYC  H8   C04  C08  111.22  3.000
 XYC  C05  C04  C08  101.43  3.000
 XYC  H8   C04  CB   108.63  3.000
 XYC  C05  C04  CB   113.39  3.000
 XYC  C08  C04  CB   111.13  3.000
 XYC  H10  C08  H9   106.95  3.000
 XYC  H10  C08  C07  112.66  3.000
 XYC  H9   C08  C07  109.94  3.000
 XYC  H10  C08  C04  112.88  3.000
 XYC  H9   C08  C04  109.38  3.000
 XYC  C07  C08  C04  105.03  3.000
 XYC  H12  C07  H11  106.33  3.000
 XYC  H12  C07  C06  110.67  3.000
 XYC  H11  C07  C06  112.00  3.000
 XYC  H12  C07  C08  110.87  3.000
 XYC  H11  C07  C08  111.41  3.000
 XYC  C06  C07  C08  105.65  3.000
 XYC  H14  C06  H13  106.35  3.000
 XYC  H14  C06  C05  110.64  3.000
 XYC  H13  C06  C05  111.70  3.000
 XYC  H14  C06  C07  110.52  3.000
 XYC  H13  C06  C07  112.22  3.000
 XYC  C05  C06  C07  105.48  3.000
 XYC  H16  C05  H15  106.59  3.000
 XYC  H16  C05  C06  109.89  3.000
 XYC  H15  C05  C06  112.80  3.000
 XYC  H16  C05  C04  108.90  3.000
 XYC  H15  C05  C04  113.87  3.000
 XYC  C06  C05  C04  104.75  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 XYC  Var_01  C06  C07  C08  C04  23.26  30.0  1
 XYC  Var_02  C05  C06  C07  C08   2.20  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XYC  chir_01  CA   N    CB  C    negativ
 XYC  chir_02  C04  C08  CB  C05  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 XYC  plan-1  O    0.020
 XYC  plan-1  C    0.020
 XYC  plan-1  CA   0.020
 XYC  plan-1  OXT  0.020

